Imaging and manipulating the structural machinery of living cells on the micro- and nanoscale

The structure, physiology, and fate of living cells are all highly sensitive to mechanical forces in the cellular microenvironment, including stresses and strains that originate from encounters with the extracellular matrix (ECM), blood and other flowing materials, and neighbouring cells. This relationship between context and physiology bears tremendous implications for the design of cellular micro-or nanotechnologies, since any attempt to control cell behavior in a device must provide the appropriate physical microenvironment for the desired cell behavior. Cells sense, process, and respond to biophysical cues in their environment through a set of integrated, multi-scale structural complexes that span length scales from single molecules to tens of microns, including small clusters of force-sensing molecules at the cell surface, micron-sized cell-ECM focal adhesion complexes, and the cytoskeleton that permeates and defines the entire cell. This review focuses on several key technologies that have recently been developed or adapted for the study of the dynamics of structural micro-and nanosystems in living cells and how these systems contribute to spatially-and temporally-controlled changes in cellular structure and mechanics. We begin by discussing subcellular laser ablation, which permits the precise incision of nanoscale structural elements in living cells in order to discern their mechanical properties and contributions to cell structure. We then discuss fluorescence recovery after photobleaching and fluorescent speckle microscopy, two live-cell fluorescence imaging methods that enable quantitative measurement of the binding and transport properties of specific proteins in the cell. Finally, we discuss methods to manipulate cellular structural networks by engineering the extracellular environment, including microfabrication of ECM distributions of defined geometry and microdevices designed to measure cellular traction forces at micron-scale resolution. Together, these methods form a powerful arsenal that is already adding significantly to our understanding of the nanoscale architecture and mechanics of living cells and may contribute to the rational design of new cellular micro-and nanotechnologies

Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications

Determinants of urinary 1-hydroxypyrene glucuronide in South Korean children.

OBJECTIVES: This study was conducted to investigate the dominant sources of the urinary pyrene metabolite, 1-hydroxypyrene glucuronide (1-OHPG), in South Korean children. METHODS: Urine samples were collected from 102 non-smoking children (aged 10-14). Urinary 1-OHPG was assayed by synchronous fluorescence spectroscopy, following immuno-affinity purification using monoclonal antibody 8E11. Urinary cotinine, a metabolite of nicotine, was measured by GC/MS. Information on environmental tobacco smoke (ETS) exposure, diet, fuel type for heating home, and other possible sources of PAH exposure was collected by self-administered questionnaires. RESULTS: Mean (+/-SE) 1-OHPG levels were 1.64 (+/-0.06) ng/ml (range 0.04-3.27 ng/ml). Two multiple linear regression analyses (differing in how ETS was approximated: by parental smoking or urinary cotinine) revealed a positive association between urinary 1-OHPG levels and parental smoking at home (P = 0.007), log urinary cotinine (P = 0.165), frequent grilled (shell)fish consumption (P = 0.061), and living in a commercial/other zone (P = 0.007) versus a residential or industrial zone. No consistent associations were found between 1-OHPG and the child's sex, grilled meat consumption, or fuels used to heat the home. CONCLUSIONS: These results support that ETS, frequent grilled fish consumption, and the ambient environment are important predictors of urinary 1-OHPG levels in South Korean children

Discovery of selective dengue virus inhibitors using combination of molecular fingerprint-based virtual screening protocols, structure-based pharmacophore model development, molecular dynamics simulations and in vitro studies

Dengue virus is a major issue of tropical and sub-tropical regions. The proliferation of virus results in immense number of deaths each year because of unavailability of on-shelf drugs. This issue necessitates the design of novel anti-Dengue drugs. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of Dengue virus. Keeping in mind the worsening situation regarding Dengue virus, approximately eighteen million drug-like compounds from the ZINC small molecule database have been screened against Nonstructural Protein 3 (NS3) previously by our group. In this study, in order to investigate the effect of extended time of molecular dynamics (MD) simulations on structural and dynamical profiles of used complexes, simulation run time is increased from 50-ns to 100-ns for the each system. In addition, a well-known Dengue virus inhibitor (MB21) from literature is used as reference structure (positive control) to compare the proposed molecules. Post-processing MD analyses including Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations were conducted to predict binding free energies of inhibitors from derived trajectory frames of MD simulations. Identified compounds are further directed to Quantum-Polarized Ligand Docking (QPLD), molecular fingerprint-based virtual screening of another small molecule database (Otava Drug Like small molecule database), and Structure-based Pharmacophore Modeling (E-Pharmacophore). Finally, cell proliferation and cytotoxicity tests as well as pre- and post-treatment on HUH7 cells infected with DENV2 NGC strain are applied for four identified hit molecules (ZINC36681949, ZINC44921800, ZINC95518765 and ZINC39500661) to check whether these drugs inhibit DENV2 from entry and/or exit pathways. Based on cell-based Dengue quantification assays, there is no effect seen on pre-treatment of cells with these compounds indicating that the early infection processes of virus is not affected. In contrast, the post-treatment of cells with these compounds after Dengue virus infection has resulted in a significant 1 log PFU/ml reduction of the virus infectious titre. © 2017 Elsevier Inc

Evaluation of Glucosinolate Variation in a Collection of Turnip (Brassica rapa) Germplasm by the Analysis of Intact and Desulfo Glucosinolates

Glucosinolates (GLS) are secondary metabolites occurring in cruciferous species. These compounds are important for plant defense, human health, and the characteristic flavor of Brassica vegetables. In this study, the GLS in tubers from a collection of 48 turnip (Brassica rapa) accessions from different geographic origin were analyzed. Two different methods were used: desulfo GLS were analyzed by high-performance liquid chromatography with a photodiode array detector, and intact GLS were analyzed by accurate mass liquid chromatography–mass spectrometry. For most GLS, desulfo and intact signals correlated well, and the analytical reproducibility for individual GLS was similar for both methods. A total of 11 different GLS was monitored in the turnip tubers, through both intact and desulfo GLS analysis methods. Four clusters of accessions could be clearly distinguished based on GLS composition of the turnip tuber. Clustering based on tuber GLS differed markedly from a previously published clustering based on leaf GLS

Evaluation of Glucosinolate Variation in a Collection of Turnip (Brassica rapa) Germplasm by the Analysis of Intact and Desulfo Glucosinolates

Glucosinolates (GLS) are secondary metabolites occurring in cruciferous species. These compounds are important for plant defense, human health, and the characteristic flavor of Brassica vegetables. In this study, the GLS in tubers from a collection of 48 turnip (Brassica rapa) accessions from different geographic origin were analyzed. Two different methods were used: desulfo GLS were analyzed by high-performance liquid chromatography with a photodiode array detector, and intact GLS were analyzed by accurate mass liquid chromatography–mass spectrometry. For most GLS, desulfo and intact signals correlated well, and the analytical reproducibility for individual GLS was similar for both methods. A total of 11 different GLS was monitored in the turnip tubers, through both intact and desulfo GLS analysis methods. Four clusters of accessions could be clearly distinguished based on GLS composition of the turnip tuber. Clustering based on tuber GLS differed markedly from a previously published clustering based on leaf GLS

RNAi screen reveals a role of SPHK2 in dengue virus–mediated apoptosis in hepatic cell lines

10.1371/journal.pone.0188121PLoS ONE1211e018812

Vitamin E TPGS-emulsified poly(lactic-co-glycolic acid) nanoparticles for cardiovascular restenosis treatment

10.2217/17435889.2.3.333Nanomedicine23333-34

Mosquito Cellular Factors and Functions in Mediating the Infectious entry of Chikungunya Virus

10.1371/journal.pntd.0002050PLoS Neglected Tropical Diseases72e205

Evaluation of plasma brain-derived neurotrophic factor levels and self-perceived cognitive impairment post-chemotherapy: A longitudinal study

10.1186/s12885-017-3861-9BMC Cancer17186